4-129708851-T-C

Position:

• chr4-129708851-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653915.1(LINC02466):​n.354+15659A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,190 control chromosomes in the GnomAD database, including 737 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.057 (737 hom., cov: 32)
• Consequence: LINC02466 ENST00000653915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LINC02466 (HGNC:53405): (long intergenic non-protein coding RNA 2466)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02466	ENST00000653915.1	n.354+15659A>G		intron_variant, non_coding_transcript_variant
LINC02466	ENST00000654715.1	n.558-12501A>G		intron_variant, non_coding_transcript_variant
LINC02466	ENST00000665329.1	n.280-12501A>G		intron_variant, non_coding_transcript_variant
LINC02466	ENST00000669328.1	n.284+18071A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8697 AN: 152074 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0233

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00205

Gnomad OTH AF: 0.0464

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0573 AC: 8724 AN: 152190 Hom.: 737 Cov.: 32 AF XY: 0.0573 AC XY: 4265 AN XY: 74438

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.0632

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00205

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0303 Hom.: 36

Bravo AF: 0.0641

Asia WGS AF: 0.100 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1491148; hg19: chr4-130630006;